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ShareScore release 0.9.0
Dataset results
9 results for “organic ligands”
A Ligand Field Molecular Mechanics Study of CO2 Induced Breathing in the metal-organic framework DUT-8(Ni)
<p>Raw Data, scripts and processed data for the publication "A Ligand Field Molecular Mechanics Study of CO2 Induced Breathing in metal-organic framework DUT-8(Ni)"</p>
Code for manuscript "Organic ligands in whale excrement support iron availability and reduce copper toxicity to the surface ocean" by Monreal et al.
<p>.zip file containing GitHub repository titled "ligands-in-whale-excrement" (<a href="https://github.com/patrickmon38/ligands-in-whale-excrement/tree/main">https://github.com/patrickmon38/ligands-in-whale-excrement/tree/main</a>)<br><br><strong>README from GitHub: </strong></p> <div> <h3>Code used to generate figures for the manuscript "Organic ligands in whale excrement support iron availability and reduce copper toxicity to the surface ocean" by Monreal et al. are found in this repository.</h3> </div> <div> <p>In press at Communications Earth & Environment</p> <p> </p> </div> <p>Most data (all except .mzXML data) called in code is from Github_Data_For_Whale_Ligand_Manuscript.xlsx in this repository.</p> <p> </p> <p>Mass spec data from .mzXML files are has been depositied and is available for download in the Mass Spectrometry Interactive Virtual Environment (MassIVE). LC-ESI-MS (Orbitrap) and LC-FT-ICR-MS raw data can be accessed there under MSV000094994 (doi:10.25345/C50000B5D) and MSV000094995 (doi:10.25345/C5V98034P), respectively.</p> <p> </p> <p>html output from Rmarkdown file can be viewed directly at <a href="https://html-preview.github.io/?url=https://github.com/patrickmon38/ligands-in-whale-excrement/blob/main/Figures_for_GitHub_Whale_Excrement_Manuscript.html" rel="nofollow">https://html-preview.github.io/?url=https://github.com/patrickmon38/ligands-in-whale-excrement/blob/main/Figures_for_GitHub_Whale_Excrement_Manuscript.html</a>.</p> <p>If trying to run Rmarkdown on your own system, you will need to download the .xlsx and .mzXML files and change paths accordingly.</p> <p>Co-authors of this manuscript:</p> <h5>Patrick J. Monreal (University of Washington)</h5> <h5>Matthew S. Savoca (Stanford University)</h5> <h5>Lydia Babcock-Adams (National High Magnetic Field Laboratory)</h5> <h5>Laura E. Moore (University of Washington)</h5> <h5>Angel Ruacho (Univesrity of Washington)</h5> <h5>Dylan Hull (University of Washington)</h5> <h5>Logan J. Pallin (Unversity of California, Santa Cruz)</h5> <h5>Ross C. Nichols (Unversity of California, Santa Cruz)</h5> <h5>John Calambokidis (Cascadia Research Collective)</h5> <h5>Joseph A. Resing (Unviersity of Washington/CICOES/NOAA)</h5> <h5>Ari S. Friedlaender (Unversity of California, Santa Cruz)</h5> <h5>Jeremy Goldbogen (Stanford University)</h5> <h5>Randelle M. Bundy (University of Washington)</h5> <p> </p> <div> </div> <div><strong>If there are issues or questions with the code, author for contact is Patrick Monreal (<a href="mailto:pmonreal@uw.edu">pmonreal@uw.edu</a>).</strong></div>
Binding constants of clinical drugs and other organic ligands with human and mammalian serum albumins
<p>The dataset contains literature values of the experimental equilibrium binding constants of drugs and some other organic ligands with human and mammalian (predominantly bovine) serum albumins. There are 1755 records gathered from 346 original literature sources describing the albumin affinity of 324 different substances. The data were extracted from both articles and existing protein binding databases applying strict data selection rules in order to exclude the values influenced by the third-party compounds. For each experiment with a particular ligand–albumin system found in literature we provide (if possible) the following details: albumin source organism, ligand chemical name, canonical SMILES, InChIKey, the binding (either association <em>K<sub>a</sub></em> or dissociation <em>K<sub>d</sub></em>) constant value in molarity-based scale, temperature in K, albumin and ligand concentrations, buffer pH, composition, and concentration, experimental method, model used for the binding constant calculation, DOI or link to the source paper. For the results obtained using independent binding sites model, the average number of binding sites <em>n</em> is also provided. If two different types of binding sites were suggested, we put the second site-specific binding constant <em>K<sub>a2</sub></em> or <em>K<sub>d2</sub></em> and the number of the second-type sites<em> </em> <em>n</em><sub>2</sub> into separate columns. For some systems, the enthalpies of binding have also been determined either from the temperature dependence of the binding constant or using direct calorimetric measurements. Their values are also given in the respective column. The dataset can be used as the reference one, for the development of predictive models to calculate the binding constants, and for the choice of the experimental setup in the future albumin binding studies.</p>
FRidge GA13 Organic Ligands CSV data
<p>Competitive Ligand Exchange-Adsorptive Cathodic Stripping Voltammetry samples from 11 sites along the Mid-Atlantic Ridge. Samples were collected as part of the 2017-18 FRidge (GA 13) research expedition on board the RSS James Cook.</p>
Potentiometric data for determination of Ge(IV) complexes with low molecular weight organic O/N-donor ligands
<p>Contains an archive of potentiometric titration data that served to determine the stability constants of Ge(IV) complexes with small organic O/N donor ligands. Files are in machine readable XML, generated by HYPERQUAD 6.0.1 (Protonic Software, UK). Data may be extracted from the files manually for use by other modeling codes. An annotated model file is provided to explain the structure of the files and a 'READ_ME' file with further info. </p>
Organizing Structural Principles of the Interleukin-17 Ligand-Receptor Axis - Single molecule tracking - raw data
<p>This dataset contains the raw image data that was analyzed in the manuscript "Organizing Structural Principles of the Interleukin-17 Ligand-Receptor Axis"</p>
Organizing Structural Principles of the Interleukin-17 Ligand-Receptor Axis - Single molecule tracking - raw data - calibration images
<p>This dataset contains the images used for channel calibration for the single molecule data that was analyzed in the manuscript "Organizing Structural Principles of the Interleukin-17 Ligand-Receptor Axis"</p>
PDB files of "Characterization of ligand-induced thermal stability of the human organic cation transporter 2 (OCT2)"
<p>The predicted alphafold structure of OCT2 (Uniprot O15244) was embedded in a DPPC model membrane, solvated with TIP3P water and subjected to 250 ns molecular dynamics simulation using the Desmond module of Schroedingers Drug Discovery Suite. The last 150 ns were used for clustering and the cluster with most of the members (cluster0) was selected as a model for OCT2. Based on that (still predicted, but optimised) model we performed docking with various substrates for which we also provide the obtained docking pose. See Publication in Frontiers in Pharmacology (DOI: 10.3389/fphar.2023.1154213) for details and results.</p>
The Notch ligand Jagged1 regulates extracellular matrix production and organization in triple-negative breast cancer
GEO Series GSE296927. Homo sapiens. 18 samples. Type: Expression profiling by high throughput sequencing.
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International Brain Laboratory public data
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OpenNeuro
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